Making his first visit to Israel, Pope Benedict XVI yesterday sought to repair frayed relations with the Jewish state by pledging to remember the millions of Jews killed in the Holocaust, saying their cry “still echoes in our hearts.”

Benedict paid his respects to the victims yesterday during a stop at Yad Vashem, Israel’s national Holocaust memorial, where the German-born pontiff shook hands and spoke to six Holocaust survivors and rekindled Yad Vashem’s eternal flame.

“I have come to stand in silence before this monument erected to honor the memory of the millions of Jews killed in the horrific tragedy of the Shoah,” he said, using the Hebrew word for Holocaust.

“May the names of these victims never perish. May their suffering never be denied, belittled or forgotten,” he said.

The 82-year-old pontiff spoke emotionally of the innocent lives lost.

“As we stand here in silence, their cry still echoes in our hearts,” he said.

Benedict’s stop at Yad Vashem did not include a visit to the main part of the museum, where a photo caption says World War II-era Pope Pius XII did not protest the Nazi genocide of Jews and maintained a largely “neutral position.”

Israel and the Vatican are at odds over the legacy of Pius, a candidate for sainthood. Benedict has called Pius a great churchman, and has praised what he said was Pius’ “courageous and paternal dedication” in trying to save Jews by quiet diplomacy.

Rabbi Israel Meir Lau, chairman of Yad Vashem’s board of directors and a former chief rabbi of Israel, called the speech important, but said he found it lacking.

“There is a clear difference between ‘killed’ and ‘murdered.’ There is a difference between saying millions in the Holocaust and saying 6 million. The word ‘six’ was not said,” Lau, a Holocaust survivor, told Israel TV. “There was certainly no apology here.”

Earlier, during an airport welcome, Benedict’s calls for the establishment of a Palestinian homeland put a damper on the trip — just the second official visit to Israel by a pope — by putting him at odds with Israel’s new government.

Benedict did, however, receive an extraordinarily warm welcome, replete with a red carpet, choir, children waving flags and red carnations, and a new strain of wheat named after him. It was presented by Israel’s president, Shimon Peres.

“In you, we see a promoter of peace, a great spiritual leader,” said Peres, who gave Benedict a Hebrew text of the Bible inscribed on a tiny silicon particle using nanotechnology.

The region’s politics intruded a short time later, when a Palestinian cleric, Taysir Tamimi, grabbed the microphone at an interfaith gathering and gave a speech blasting Israel’s recent war in Gaza and its occupation of the West Bank.

Tamimi, the head of the Islamic courts in the West Bank and Gaza, ignored attempts by a Christian clergyman to persuade him to leave the podium. The Vatican issued a condemnation, saying that “this intervention was a direct negation of what dialogue should be.”